In the three-day event played over Yorkshire’s trio of Ryder Cup venues – Ganton, Lindrick and Moortown – they compiled 131pts to overhaul second-round leaders Michael Williams and Guy Henderson (Eaglescliffe) and win by four.
Third place went to Lindrick’s Thomas and James Wolstenholme on 126.
Knowles and Pethybridge, who were tied for third after 36 holes having scored 42pts at Moortown and 43 at Lindrick, had three birdies in their first four holes on the final day at Ganton and another at the seventh.
Knowles then birdied the 501-yard par-5 ninth for a net eagle that took them to 24pts for the outward run.
They replicated their start to the round by grabbing three birdies in the first four holes on the way back to the clubhouse, two more at 15 and 17 sandwiching their only one-pointer.
Williams and Henderson – whose lead after day two was the result of garnering 43pts at Lindrick and 45 at Ganton – racked up four birdies in their first half a dozen holes at Moortown before stumbling to a one-pointer at the seventh.
They began the back nine with a birdie, but this and another at 16 were negated by one-pointers at 14 and 17.
The Wolstenholmes made the most of home knowledge on the final day, particularly on the back nine.
With 44pts at Ganton and 36 at Moortown to their name they began steadily around Lindrick until James birdied the 316-yard par-4 eighth for a net eagle.
It ignited their round and their back nine reaped a stunning 26pts made up of six birdies and a birdie/net eagle from Thomas at the 433-yard par-4 13th.
They subsequently won the Ganton Division, Williams and Henderson took the Lindrick and Knowles and Pethbridge prevailed in the Moortown.